relax SVN archive

Fix for the now read-only tensor objects - the set() method is now used to store the parameter values.

Removed a debugging printout.

Fix for the align_tensor.init user function.

This change is needed as the tensor object is now completely read-only.

Python 3 update for the external Sobol library.

The command used was:
2to3 -w extern/sobol/*

The results were manually edited afterward to clean up some mess (print with double brackets, etc).

Python 3 fix - replaced all xrange() calls with range().

Python 3 fix for the structural API.

The command used was:
2to3 -w generic_fns/structure/api_base.py

Python 3 fixes for the Frame Order testing branch.

This includes print statement removal and updates of the all raise statement syntax.

Merged revisions 17808,17812-17820 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17808 | bugman | 2012-10-15 15:01:36 +0200 (Mon, 15 Oct 2012) | 3 lines

Added support for Python 2.2 and earlier for the compilation of the C modules.
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r17812 | bugman | 2012-10-15 15:27:08 +0200 (Mon, 15 Oct 2012) | 3 lines

Python 3 fix for the compat module - the Queue2 object needs to always be defined.
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r17813 | bugman | 2012-10-15 16:35:44 +0200 (Mon, 15 Oct 2012) | 6 lines

Bug fix for the unit test runner - this restores functionality broken all the way back at r12100.

The TEST_SUITE_ROOT constant no longer exists, so the check for it is now skipped. This allows
tests to be run directly be the script.
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r17814 | bugman | 2012-10-15 16:42:07 +0200 (Mon, 15 Oct 2012) | 5 lines

Python 2.3 and earlier fix for the unit test module for the float module.

The 'tests' class variable was renamed so that the test suite does not think that it is a unit test.
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r17815 | bugman | 2012-10-15 17:14:26 +0200 (Mon, 15 Oct 2012) | 3 lines

The GUI is now cleanly exited with a call to wx.App.ExitMainLoop rather than wx.Exit.
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r17816 | bugman | 2012-10-15 17:24:36 +0200 (Mon, 15 Oct 2012) | 3 lines

Even cleaner exiting of the GUI - the interpreter thread is terminated by the exit_gui() method.
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r17817 | bugman | 2012-10-15 18:16:37 +0200 (Mon, 15 Oct 2012) | 5 lines

The text relax controller log is no longer cleared when a reset occurs.

This allows the test suite results to still be presented in GUI mode.
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r17818 | bugman | 2012-10-15 18:29:47 +0200 (Mon, 15 Oct 2012) | 10 lines

Big fixes for the running of the GUI tests.

The GUI initialisation and termination, when not running in GUI mode, is now preformed outside of
the Python unittest framework. The GUI was previously initalised in the setUp() method for all GUI
tests, but for some reason this caused abrupt terminations of the GUI_test_runner.run() method.
This run method, when finished, would not return to the Test_suite_runner but would cause the Python
interpreter to silently die. The result was that the test suite summary would appear not to be
printed out.
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r17819 | bugman | 2012-10-15 18:36:40 +0200 (Mon, 15 Oct 2012) | 3 lines

The test suite can now run again when wxPython is missing (bug from the last commit).
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r17820 | bugman | 2012-10-16 09:56:37 +0200 (Tue, 16 Oct 2012) | 3 lines

Better formatting of the test suite summary.
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Merged revisions 17780-17806 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17780 | bugman | 2012-10-09 10:26:13 +0200 (Tue, 09 Oct 2012) | 3 lines

Python 3 fix for the model-free BMRB export - many string module methods no longer exist.
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r17781 | bugman | 2012-10-09 10:29:53 +0200 (Tue, 09 Oct 2012) | 3 lines

More Python 3 fixes for the use of now non-existent string module functions.
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r17782 | bugman | 2012-10-09 11:53:02 +0200 (Tue, 09 Oct 2012) | 6 lines

All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails.

This removes a pile of useless error messages from the test, and presents a table of skipped tests
at the end.
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r17783 | bugman | 2012-10-09 12:03:29 +0200 (Tue, 09 Oct 2012) | 6 lines

Python 2.5 and lower fix for the test_write_protein_sequence() unit test.

The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the code
without failing, and the byte array comparison is now only used for Python 3+.
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r17784 | bugman | 2012-10-09 12:09:45 +0200 (Tue, 09 Oct 2012) | 5 lines

The Results system tests are no longer dependent on the relaxation curve-fitting C modules.

This allows these tests to run when the module cannot be imported.
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r17785 | bugman | 2012-10-09 12:50:29 +0200 (Tue, 09 Oct 2012) | 6 lines

Created a special script for testing out relax with Python versions 1.0 all the way to 3.3.

This builds the C modules for each Python version in ~/bin and then runs the test suite, outputting
everything to log files.
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r17786 | bugman | 2012-10-09 12:52:34 +0200 (Tue, 09 Oct 2012) | 6 lines

Python 2.4 fixes - the ctypes module does not exist in Python versions 2.4 and lower.

This is only used for some non-essential functionality on MS Windows, so now it is deactivated if
not present.
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r17787 | bugman | 2012-10-09 12:59:11 +0200 (Tue, 09 Oct 2012) | 6 lines

Python 2.4 and lower fix for the pipe_loop() generator method.

In these Python versions, a 'try' block with a 'finally' statement cannot contain 'yield'
statements! This work around should be compatible with all Python versions.
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r17788 | bugman | 2012-10-09 13:36:46 +0200 (Tue, 09 Oct 2012) | 3 lines

Fix for the test_write_protein_sequence() unit test for a recently introduced bug.
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r17789 | bugman | 2012-10-09 14:28:30 +0200 (Tue, 09 Oct 2012) | 6 lines

Reactivated support for Python 2.3.

This mainly skips the missing 'subprocess' module. This however decreases relax's functionality a
little.
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r17790 | bugman | 2012-10-09 14:35:38 +0200 (Tue, 09 Oct 2012) | 3 lines

Small improvements to the multiple python version test suite testing script.
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r17791 | bugman | 2012-10-09 15:59:34 +0200 (Tue, 09 Oct 2012) | 6 lines

Fix for the Mf.test_write_results() system test for Python 3.1.

The XML version in Python 3.1 is the old style! Therefore the old results file is being used to
check this Python 3.1 result.
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r17792 | bugman | 2012-10-09 20:47:25 +0200 (Tue, 09 Oct 2012) | 7 lines

Better Python 2.3 support.

The compat module is now imported at the very start to allow the builtins to be set before any other
imports. The sorted() builtin method is now mimicked and the os.devnull string set for Python 2.3
and earlier.
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r17793 | bugman | 2012-10-09 20:59:17 +0200 (Tue, 09 Oct 2012) | 3 lines

Python 2.4 fix - the unit test runner no longer uses the builtin set() method.
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r17794 | bugman | 2012-10-09 21:06:42 +0200 (Tue, 09 Oct 2012) | 5 lines

Python 2.4 and earlier fix for the GUI.

Try-except-finally statement blocks are not supported, so these have to nested in two try statements.
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r17795 | bugman | 2012-10-10 16:37:34 +0200 (Wed, 10 Oct 2012) | 6 lines

Fix for the Mf.test_write_results() system test for the Python 3 versions.

The logic for determining Python 3 versions was broken and the incorrect files was used for Python
3.1.
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r17796 | bugman | 2012-10-10 16:44:00 +0200 (Wed, 10 Oct 2012) | 6 lines

Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.

The object comparison method no longer converts dictionaries to strings for the comparison, as the
string version is different in different Python versions.
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r17797 | bugman | 2012-10-11 10:53:47 +0200 (Thu, 11 Oct 2012) | 5 lines

Disabled the initial relax intro print out from the GUI when running the test suite.

This prevents the intro text from appearing in the first failed test.
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r17798 | bugman | 2012-10-12 11:48:22 +0200 (Fri, 12 Oct 2012) | 10 lines

Redesigned the reset user function backend.

This now no only clears out the relax data store, but it also resets the GUI if present. Some of
the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI
window are closed and the relax controller gauges are set to zero and the log window text cleared.

These changes should allow GUI tests after an error or failure to pass, something which is currently
problematic.
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r17799 | bugman | 2012-10-15 10:21:37 +0200 (Mon, 15 Oct 2012) | 6 lines

Python 3 fix for the ScientificPython PDB reader unit tests.

The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now
they are sorted prior to comparison.
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r17800 | bugman | 2012-10-15 10:31:28 +0200 (Mon, 15 Oct 2012) | 3 lines

Python 2.3 fix - eliminated the superfluous operator.itemgetter() call in the diffusion tensor code.
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r17801 | bugman | 2012-10-15 10:39:20 +0200 (Mon, 15 Oct 2012) | 5 lines

Python 2.3 and earlier fix - the subprocess module is only imported when present.

This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.
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r17802 | bugman | 2012-10-15 10:42:56 +0200 (Mon, 15 Oct 2012) | 5 lines

Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.

The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.
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r17803 | bugman | 2012-10-15 10:48:09 +0200 (Mon, 15 Oct 2012) | 3 lines

Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped if the subprocess module is missing.
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r17804 | bugman | 2012-10-15 13:50:51 +0200 (Mon, 15 Oct 2012) | 7 lines

Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.

This allows the test suite to terminate normally. With different Python versions on different
operating systems, this could sometimes cause the test suite to freeze at the end, the final
printout to be missing, or other strange behaviour.
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r17805 | bugman | 2012-10-15 14:24:14 +0200 (Mon, 15 Oct 2012) | 3 lines

Removed an unused import of the Queue module from the multi-processor.
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r17806 | bugman | 2012-10-15 14:25:51 +0200 (Mon, 15 Oct 2012) | 7 lines

Python 2.4 and earlier fixes for the Queuing module.

The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+
has been added to the compat module. This module is now used for all imports of the Queue class for
all Python versions.
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Merged revisions 17776-17778 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17776 | bugman | 2012-10-09 00:59:53 +0200 (Tue, 09 Oct 2012) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-17738" from
svn+ssh://bugman@.../svn/relax/branches/tensor_data
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r17777 | bugman | 2012-10-09 01:01:34 +0200 (Tue, 09 Oct 2012) | 180 lines

Merged revisions 17739-17774 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/tensor_data

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r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines

The diffusion tensor data structure has been completely converted into a read-only structure.

The __setattr__() method now will always raise a RelaxError, and the diffusion tensor simulation
data structure objects __setitem__() method will raise the same error.
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r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the initialisation of the diffusion tensor data structure, now that it is read-only.
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r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines

The new diffusion tensor fixed() method has been created to allow the fixed flag to be changed.
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r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines

Created the diffusion tensor data structure type() method for setting the tensor type.

This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of relax, as the structure is
now read only.
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r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines

Renamed the diffusion tensor data structure type() method to set_type().

This is because the type is stored as the 'type' object, clashing with the method name.
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r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines

Converted the old diffusion tensor __setattr__() method into the set() method.

This is the only way in which diffusion tensor parameters, errors and simulations can be set.
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r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines

Improvements to the diffusion tensor set() method.

The parameters, errors and simulations are now properly differentiated and stored.
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r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines

A number of private diffusion tensor objects and methods have switched to the single leading '_' format.
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r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines

Removed all the unused imports from specific_fns.model_free.main.
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r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

Redesigned how diffusion tensor simulation structures are handled.

The design is now much cleaner and works with all Python versions.
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r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines

Modified the setUp() method for the diffusion tensor system tests to use the new design.
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r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines

The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.
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r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the diffusion tensor __deepcopy__() replacement method for the new design.
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r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines

The setting of list values for the DiffTensorSimList object now works correctly.

The private _set() method now works correctly by calling the base class method, and the normal
setting of diffusion tensor simulation values produces a RelaxError.
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r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines

Fix for the Diffusion_tensor.test_copy system test - the simulation parameters are now read-only.

Instead, the diffusion tensor set() method needs to be called.
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r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines

Converted the diffusion tensor data structure from_xml() method to the new tensor design.
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r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines

Fix for the diffusion tensor to_xml() method for the new design.

For some reason the methods of the Element class are no longer blacklisted.
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r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines

Fix for the model-free specific analysis duplicate_data() method for the new design.

The diffusion tensor __mod_attr__ object is now called _mod_attr.
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r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines

Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.
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r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines

The fix user function now uses the diffusion tensor set_fixed() method.
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r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines

The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().
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r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines

Converted the palmer.extract user function to use the new diffusion tensor design.
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r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines

Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.

This was the previous behaviour and is needed for the test suite to pass.
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r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

Fix for the fixing of parameters in the model-free analyses.

The diffusion tensor set_fixed() method is now used.
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r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines

Another fix for the diffusion_tensor.init user function - it was not completely converted.
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r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.
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r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.
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r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines

Another fix for the fold_angles() diffusion tensor function - again an incomplete design conversion.
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r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the reading of relax 1.2 model-free results files for the diffusion tensor structure redesign.
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r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines

Fix for the reading of model-free results files from relax 1.2 when simulation data is missing.
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r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines

Updated all of the diffusion tensor unit tests to the new design.
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r17770 | bugman | 2012-10-08 22:36:00 +0200 (Mon, 08 Oct 2012) | 3 lines

Cleaned up the docstring of the diffusion tensor data object __setattr__() method.
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r17771 | bugman | 2012-10-08 22:36:47 +0200 (Mon, 08 Oct 2012) | 3 lines

Removed the now unused _update_sim_append() method from the diffusion tensor data structure.
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r17772 | bugman | 2012-10-08 22:38:18 +0200 (Mon, 08 Oct 2012) | 3 lines

Deleted the now unused _update_sim_set() method of the diffusion tensor data structure.
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r17773 | bugman | 2012-10-08 22:49:38 +0200 (Mon, 08 Oct 2012) | 3 lines

Small clean ups of the diffusion tensor data structure code.
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r17774 | bugman | 2012-10-09 00:24:34 +0200 (Tue, 09 Oct 2012) | 7 lines

Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensor.

This large set of changes matches all of those revisions for the diffusion tensor already committed in
this branch. The alignment tensor data structures are now read only, and can only be modified via the
set() method. This is a much simplified design which works on all Python versions.
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r17778 | bugman | 2012-10-09 01:02:04 +0200 (Tue, 09 Oct 2012) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/tensor_data
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